Locus 9815

Sequence ID	dm3.chr3R
Location	9,289,944 – 9,290,026
Length	82
Max. P	0.999264

overview

Window 9

Location	9,289,944 – 9,290,026
Length	82
Sequences	14
Columns	90
Reading direction	forward
Mean pairwise identity	88.48
Shannon entropy	0.26611
G+C content	0.50874
Mean single sequence MFE	-30.51
Consensus MFE	-25.02
Energy contribution	-25.48
Covariance contribution	0.46
Combinations/Pair	1.16
Mean z-score	-3.45
Structure conservation index	0.82
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.27
SVM RNA-class probability	0.998155
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9289944 82 + 27905053
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCGA
..((((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..)))))). ( -33.72, z-score =  -4.06, R)
>droGri2.scaffold_14906 3807837 82 + 14172833
GUCGCCUUAAUAAGCACUUGGGCAGCAGGAGGCAUUGCGGACACAAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCAA
...((.((..((((.(((...((.(((((((((...))((.......))...--------))))))).))...))).))))..)).)).. ( -26.30, z-score =  -1.79, R)
>droMoj3.scaffold_6540 10349278 82 + 34148556
GUCGCUUUGAUAAGCACUUGGGCAGCAGGAGGCAUUGCGGACACAACCCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCAA
...(((((..((((.(((...((.(((((((.....(.((......)))...--------))))))).))...))).))))..))))).. ( -30.40, z-score =  -2.82, R)
>droVir3.scaffold_12855 7299611 82 - 10161210
GUCGCUUUAAUAAGCACUUGGGCAGCAGGAGGCAUUGCGGACACAAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCAA
...(((((..((((.(((...((.(((((((((...))((.......))...--------))))))).))...))).))))..))))).. ( -30.40, z-score =  -3.56, R)
>droSim1.chr3R_random 533445 82 + 1307089
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCGA
..((((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..)))))). ( -33.72, z-score =  -4.06, R)
>droWil1.scaffold_181130 6363229 82 + 16660200
GUCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUACGGACACGAACCAAA--------CUCCUGCGGCACUAGUACUUAGUAAAGCAA
...((((((.((((.(((...((.(((((((......((....)).......--------))))))).))...))).)))).)))))).. ( -30.92, z-score =  -4.51, R)
>droPer1.super_0 8163706 82 - 11822988
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCAA
...(((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..))))).. ( -31.92, z-score =  -3.61, R)
>dp4.chr2 16736635 82 + 30794189
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCAA
...(((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..))))).. ( -31.92, z-score =  -3.61, R)
>droAna3.scaffold_13340 1848681 82 + 23697760
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCGA
..((((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..)))))). ( -33.72, z-score =  -4.06, R)
>droEre2.scaffold_4770 5395799 82 - 17746568
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCGA
..((((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..)))))). ( -33.72, z-score =  -4.06, R)
>droYak2.chr3R 13598024 82 + 28832112
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCGA
..((((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..)))))). ( -33.72, z-score =  -4.06, R)
>droSec1.super_0 8405346 82 - 21120651
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA--------CUCCUGCGGCACUAGUACUUAGGAAAGCGA
..((((((..((((.(((...((.(((((((......((....)).......--------))))))).))...))).))))..)))))). ( -33.72, z-score =  -4.06, R)
>apiMel3.GroupUn 149494248 85 + 399230636
GACCCAUUGAUAAGCACUUGAGCAGCAGGAGAUAUGGUAAUUUCUAACCCAACCUAGUCACUCCUGCGGCACUAGUACUUAUGAA-----
......((.(((((.(((.(.((.(((((((....(((.............)))......))))))).)).).))).))))).))----- ( -23.02, z-score =  -2.26, R)
>anoGam1.chr2R 54489126 65 + 62725911
--CUCUUCGAUAAGCACUUGGGCAGCAGGGGUUA----------GAAUCU----------CUCCUGCGGCACUAGUACUUAGUAAAG---
--..(((...((((.(((...((.(((((((...----------......----------))))))).))...))).))))...)))--- ( -20.00, z-score =  -1.79, R)
>consensus
GCCGCUUUAAUAAGCACUUGGGCAGCAGGAGGUAUUGCGGACACGAACCUAA________CUCCUGCGGCACUAGUACUUAGGAAAGCAA
...(((((..((((.(((...((.(((((((((...))((.......))...........))))))).))...))).))))..))))).. (-25.02 = -25.48 +   0.46)

alignment

secondary structure

dotplot

Window 0

Location	9,289,944 – 9,290,026
Length	82
Sequences	14
Columns	90
Reading direction	reverse
Mean pairwise identity	88.48
Shannon entropy	0.26611
G+C content	0.50874
Mean single sequence MFE	-32.68
Consensus MFE	-29.53
Energy contribution	-29.67
Covariance contribution	0.14
Combinations/Pair	1.22
Mean z-score	-4.51
Structure conservation index	0.90
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.75
SVM RNA-class probability	0.999264
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9289944 82 - 27905053
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..))))))). ( -34.00, z-score =  -4.75, R)
>droGri2.scaffold_14906 3807837 82 - 14172833
UUGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUUGUGUCCGCAAUGCCUCCUGCUGCCCAAGUGCUUAUUAAGGCGAC
(((((((..((((((((.(.((.((((((.--------...(((((((....)))).))))))))).)).).))))))))..))))))). ( -33.90, z-score =  -4.31, R)
>droMoj3.scaffold_6540 10349278 82 - 34148556
UUGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGGUUGUGUCCGCAAUGCCUCCUGCUGCCCAAGUGCUUAUCAAAGCGAC
(((((((..((((((((.(.((.(((((((--------...(.(((((....))))).)))))))).)).).))))))))..))))))). ( -36.70, z-score =  -5.21, R)
>droVir3.scaffold_12855 7299611 82 + 10161210
UUGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUUGUGUCCGCAAUGCCUCCUGCUGCCCAAGUGCUUAUUAAAGCGAC
(((((((..((((((((.(.((.((((((.--------...(((((((....)))).))))))))).)).).))))))))..))))))). ( -34.20, z-score =  -5.12, R)
>droSim1.chr3R_random 533445 82 - 1307089
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..))))))). ( -34.00, z-score =  -4.75, R)
>droWil1.scaffold_181130 6363229 82 - 16660200
UUGCUUUACUAAGUACUAGUGCCGCAGGAG--------UUUGGUUCGUGUCCGUAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGAC
((((((((.((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).)))))))).)))))))). ( -34.60, z-score =  -5.81, R)
>droPer1.super_0 8163706 82 + 11822988
UUGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
.((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..)))))).. ( -32.00, z-score =  -3.96, R)
>dp4.chr2 16736635 82 - 30794189
UUGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
.((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..)))))).. ( -32.00, z-score =  -3.96, R)
>droAna3.scaffold_13340 1848681 82 - 23697760
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..))))))). ( -34.00, z-score =  -4.75, R)
>droEre2.scaffold_4770 5395799 82 + 17746568
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..))))))). ( -34.00, z-score =  -4.75, R)
>droYak2.chr3R 13598024 82 - 28832112
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..))))))). ( -34.00, z-score =  -4.75, R)
>droSec1.super_0 8405346 82 + 21120651
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG--------UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((--------....(((((....)).)))..))))))).)).).))))))))..))))))). ( -34.00, z-score =  -4.75, R)
>apiMel3.GroupUn 149494248 85 - 399230636
-----UUCAUAAGUACUAGUGCCGCAGGAGUGACUAGGUUGGGUUAGAAAUUACCAUAUCUCCUGCUGCUCAAGUGCUUAUCAAUGGGUC
-----...(((((((((.(.((.(((((((...(......)(((.(....).)))....))))))).)).).)))))))))......... ( -28.10, z-score =  -2.45, R)
>anoGam1.chr2R 54489126 65 - 62725911
---CUUUACUAAGUACUAGUGCCGCAGGAG----------AGAUUC----------UAACCCCUGCUGCCCAAGUGCUUAUCGAAGAG--
---((((..((((((((.(.((.(((((..----------......----------.....))))).)).).))))))))..))))..-- ( -22.02, z-score =  -3.83, R)
>consensus
UCGCUUUCCUAAGUACUAGUGCCGCAGGAG________UUAGGUUCGUGUCCGCAAUACCUCCUGCUGCCCAAGUGCUUAUUAAAGCGGC
(((((((..((((((((.(.((.(((((((...........((.......)).......))))))).)).).))))))))..))))))). (-29.53 = -29.67 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:11:43 2011